bio::phylonetwork::treefactorymulti(3pm) [debian man page]
Bio::PhyloNetwork::TreeFactoryMulti(3pm) User Contributed Perl Documentation Bio::PhyloNetwork::TreeFactoryMulti(3pm) NAME
Bio::PhyloNetwork::TreeFactoryMulti - Module to sequentially generate Phylogenetic Trees SYNOPSIS
use strict; use warnings; use Bio::PhyloNetwork; use Bio::PhyloNetwork::TreeFactory; # Will generate sequentially all the 15 binary phylogetic # trees with 4 leaves my $factory=Bio::PhyloNetwork::TreeFactory->new(-numleaves=>4); my @nets; while (my $net=$factory->next_network()) { push @nets,$net; print "".(scalar @nets).": ".$net->eNewick()." "; } DESCRIPTION
Sequentially builds a (binary) phylogenetic tree each time next_network is called. AUTHOR
Gabriel Cardona, gabriel(dot)cardona(at)uib(dot)es SEE ALSO
Bio::PhyloNetwork APPENDIX
The rest of the documentation details each of the object methods. new Title : new Usage : my $factory = new Bio::PhyloNetwork::TreeFactory(); Function: Creates a new Bio::PhyloNetwork::TreeFactory Returns : Bio::PhyloNetwork::RandomFactory Args : -numleaves => integer OR -leaves => reference to an array (of leaves names) Returns a Bio::PhyloNetwork::TreeFactory object. Such an object will sequentially create binary phylogenetic trees each time next_network is called. If the parameter -leaves=>@leaves is given, then the set of leaves of these networks will be @leaves. If it is given the parameter -numleaves=>$numleaves, then the set of leaves will be "l1"..."l$numleaves". next_network Title : next_network Usage : my $net=$factory->next_network() Function: returns a tree Returns : Bio::PhyloNetwork Args : none perl v5.14.2 2012-03-02 Bio::PhyloNetwork::TreeFactoryMulti(3pm)
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Bio::PhyloNetwork::Factory(3pm) User Contributed Perl Documentation Bio::PhyloNetwork::Factory(3pm) NAME
Bio::PhyloNetwork::Factory - Module to sequentially generate Phylogenetic Networks SYNOPSIS
use strict; use warnings; use Bio::PhyloNetwork; use Bio::PhyloNetwork::Factory; # Will generate sequentially all the 4059 binary tree-child phylogenetic # networks with 4 leaves my $factory=Bio::PhyloNetwork::Factory->new(-numleaves=>4); my @nets; while (my $net=$factory->next_network()) { push @nets,$net; print "".(scalar @nets).": ".$net->eNewick()." "; } DESCRIPTION
Sequentially builds a (binary tree-child) phylogenetic network each time next_network is called. AUTHOR
Gabriel Cardona, gabriel(dot)cardona(at)uib(dot)es SEE ALSO
Bio::PhyloNetwork APPENDIX
The rest of the documentation details each of the object methods. new Title : new Usage : my $factory = new Bio::PhyloNetwork::Factory(); Function: Creates a new Bio::PhyloNetwork::Factory Returns : Bio::PhyloNetwork::RandomFactory Args : -numleaves => integer OR -leaves => reference to an array (of leaves names) -numhybrids => integer [default = numleaves -1] -recurse => boolean [optional] Returns a Bio::PhyloNetwork::Factory object. Such an object will sequentially create binary tree-child phylogenetic networks each time next_network is called. If the parameter -leaves=>@leaves is given, then the set of leaves of these networks will be @leaves. If it is given the parameter -numleaves=>$numleaves, then the set of leaves will be "l1"..."l$numleaves". If the parameter -numhybrids=>$numhybrids is given, then the generated networks will have at most $numhybrids hybrid nodes. Note that, necessarily, $numhybrids < $numleaves. If the parameter -recurse=>1 is given, then all networks with number of hybrid nodes less or equal to $numhybrids will be given; otherwise only those with exactly $numhybrids hybrid nodes. next_network Title : next_network Usage : my $net=$factory->next_network() Function: returns a network Returns : Bio::PhyloNetwork Args : none perl v5.14.2 2012-03-02 Bio::PhyloNetwork::Factory(3pm)